X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=11d9f68076f835e9ec4a2a770822ae1ffe973d20;hb=16887ff26b068405a235a6a8a37f4e62516de393;hp=8497a5f7c84be3ea25ebf2d16ef6ddde3eeefc95;hpb=5740f3482ac603ba6234e79a45701c2e864ee242;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 8497a5f7..11d9f680 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,15 +1,16 @@ -// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.18 2003/08/29 09:47:13 malaterre Exp $ +// vtkGdcmReader.cxx +//----------------------------------------------------------------------------- // ////////////////////////////////////////////////////////////// // WARNING TODO CLENAME // Actual limitations of this code: // // /////// Redundant and unnecessary header parsing // In it's current state this code actually parses three times the Dicom -// header of a file before the corrersponding image gets loaded in the +// header of a file before the corresponding image gets loaded in the // ad-hoc vtkData ! // Here is the process: // 1/ First loading happens in ExecuteInformation which in order to -// positionate the vtk extents calls CheckFileCoherence. The purpous +// positionate the vtk extents calls CheckFileCoherence. The purpose // of CheckFileCoherence is to make sure all the images in the future // stack are "homogenous" (same size, same representation...). This // can only be achieved by parsing all the Dicom headers... @@ -17,18 +18,23 @@ // 2a/ ExecuteData calls AllocateOutputData that in turn seems to // (indirectely call) ExecuteInformation which ends up in a second // header parsing +// This is fixed by adding a test at the beginning of ExecuteInformation +// on the modification of the object instance. If a modification have been +// made (method Modified() ), the MTime value is increased. The fileTime +// is compared to this new value to find a modification in the class +// parameters // 2b/ the core of ExecuteData then needs gdcmFile (which in turns -// initialiszes gdcmHeader in the constructor) in order to access +// initialises gdcmHeader in the constructor) in order to access // the data-image. // // Possible solution: // maintain a list of gdcmFiles (created by say ExecuteInformation) created // once and for all accross the life of vtkGdcmHeader (it would only load // new gdcmFile if the user changes the list). ExecuteData would then use -// those gdcmFile and hence avoid calling the consctutor: +// those gdcmFile and hence avoid calling the construtor: // - advantage: the header of the files would only be parser once. // - drawback: once execute information is called (i.e. on creation of -// a vtkGdcmHeader) the gdcmFile sctructue is loaded in memory. +// a vtkGdcmHeader) the gdcmFile structure is loaded in memory. // The average size of a gdcmHeader being of 100Ko, is one // loads 10 stacks of images with say 200 images each, you // end-up with a loss of 200Mo... @@ -37,523 +43,653 @@ // ExecuteData allocates space for the pixel data [which will get pointed // by the vtkPointData() through the call // data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0);] -// This data is never "freed" neither in the desctutor nor when the +// This data is never "freed" neither in the destructor nor when the // filename list is extended, ExecuteData is called a second (or third) // time... // ////////////////////////////////////////////////////////////// -#include +#include "gdcmFile.h" +#include "gdcmHeaderHelper.h" +#include "vtkGdcmReader.h" + +//#include #include #include #include -#include "vtkGdcmReader.h" -#include "gdcm.h" +#include + +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.46 $"); +vtkStandardNewMacro(vtkGdcmReader); +//----------------------------------------------------------------------------- +// Constructor / Destructor vtkGdcmReader::vtkGdcmReader() { - // Constructor + this->LookupTable = NULL; + this->AllowLookupTable = 0; } -//---------------------------------------------------------------------------- vtkGdcmReader::~vtkGdcmReader() -{ - this->RemoveAllFileName(); - this->InternalFileNameList.clear(); +{ + this->RemoveAllFileName(); + this->InternalFileNameList.clear(); + if(this->LookupTable) + this->LookupTable->Delete(); +} + +//----------------------------------------------------------------------------- +// Print +void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) +{ + vtkImageReader::PrintSelf(os,indent); + os << indent << "Filenames : " << endl; + vtkIndent nextIndent = indent.GetNextIndent(); + for (std::list::iterator FileName = FileNameList.begin(); + FileName != FileNameList.end(); + ++FileName) + { + os << nextIndent << FileName->c_str() << endl ; + } } -//---------------------------------------------------------------------------- -// Remove all files from the list of images to read. +//----------------------------------------------------------------------------- +// Public +/* + * Remove all files from the list of images to read. + */ void vtkGdcmReader::RemoveAllFileName(void) { - this->FileNameList.clear(); + this->FileNameList.clear(); + this->Modified(); } -//---------------------------------------------------------------------------- -// Adds a file name to the list of images to read. +/* + * Adds a file name to the list of images to read. + */ void vtkGdcmReader::AddFileName(const char* name) { - // We need to bypass the const pointer [since list<>.push_bash() only - // takes a char* (but not a const char*)] by making a local copy: - char * LocalName = new char[strlen(name) + 1]; - strcpy(LocalName, name); - this->FileNameList.push_back(LocalName); - this->Modified(); - delete[] LocalName; + // We need to bypass the const pointer [since list<>.push_bash() only + // takes a char* (but not a const char*)] by making a local copy: + char * LocalName = new char[strlen(name) + 1]; + strcpy(LocalName, name); + this->FileNameList.push_back(LocalName); + delete[] LocalName; + this->Modified(); } -//---------------------------------------------------------------------------- -// Sets up a filename to be read. -void vtkGdcmReader::SetFileName(const char *name) { - vtkImageReader2::SetFileName(name); - // Since we maintain a list of filenames, when building a volume, - // (see vtkGdcmReader::AddFileName), we additionaly need to purge - // this list when we manually positionate the filename. - this->FileNameList.clear(); - this->Modified(); +/* + * Sets up a filename to be read. + */ +void vtkGdcmReader::SetFileName(const char *name) +{ + vtkImageReader2::SetFileName(name); + // Since we maintain a list of filenames, when building a volume, + // (see vtkGdcmReader::AddFileName), we additionaly need to purge + // this list when we manually positionate the filename. + vtkDebugMacro("Clearing all files given with AddFileName"); + this->FileNameList.clear(); + this->Modified(); } -//---------------------------------------------------------------------------- -// Adds a file name to the internal list of images to read. -void vtkGdcmReader::RemoveAllInternalFileName(void) +//----------------------------------------------------------------------------- +// Protected +/* + * Configure the output e.g. WholeExtent, spacing, origin, scalar type... + */ +void vtkGdcmReader::ExecuteInformation() { - this->InternalFileNameList.clear(); + if(this->MTime>this->fileTime) + { + this->TotalNumberOfPlanes = this->CheckFileCoherence(); + if ( this->TotalNumberOfPlanes == 0) + { + vtkErrorMacro("File set is not coherent. Exiting..."); + return; + } + + // if the user has not set the extent, but has set the VOI + // set the z axis extent to the VOI z axis + if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 && + (this->DataVOI[4] || this->DataVOI[5])) + { + this->DataExtent[4] = this->DataVOI[4]; + this->DataExtent[5] = this->DataVOI[5]; + } + + // When the user has set the VOI, check it's coherence with the file content. + if (this->DataVOI[0] || this->DataVOI[1] || + this->DataVOI[2] || this->DataVOI[3] || + this->DataVOI[4] || this->DataVOI[5]) + { + if ((this->DataVOI[0] < 0) || + (this->DataVOI[1] >= this->NumColumns) || + (this->DataVOI[2] < 0) || + (this->DataVOI[3] >= this->NumLines) || + (this->DataVOI[4] < 0) || + (this->DataVOI[5] >= this->TotalNumberOfPlanes )) + { + vtkWarningMacro("The requested VOI is larger than expected extent."); + this->DataVOI[0] = 0; + this->DataVOI[1] = this->NumColumns - 1; + this->DataVOI[2] = 0; + this->DataVOI[3] = this->NumLines - 1; + this->DataVOI[4] = 0; + this->DataVOI[5] = this->TotalNumberOfPlanes - 1; + } + } + + // Positionate the Extent. + this->DataExtent[0] = 0; + this->DataExtent[1] = this->NumColumns - 1; + this->DataExtent[2] = 0; + this->DataExtent[3] = this->NumLines - 1; + this->DataExtent[4] = 0; + this->DataExtent[5] = this->TotalNumberOfPlanes - 1; + + // We don't need to positionate the Endian related stuff (by using + // this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian() + // since the reading of the file is done by gdcm. + // But we do need to set up the data type for downstream filters: + if ( ImageType == "8U" ) + { + vtkDebugMacro("8 bits unsigned image"); + this->SetDataScalarTypeToUnsignedChar(); + } + else if ( ImageType == "8S" ) + { + vtkErrorMacro("Cannot handle 8 bit signed files"); + return; + } + else if ( ImageType == "16U" ) + { + vtkDebugMacro("16 bits unsigned image"); + this->SetDataScalarTypeToUnsignedShort(); + } + else if ( ImageType == "16S" ) + { + vtkDebugMacro("16 bits signed image"); + this->SetDataScalarTypeToShort(); + //vtkErrorMacro("Cannot handle 16 bit signed files"); + } + else if ( ImageType == "32U" ) + { + vtkDebugMacro("32 bits unsigned image"); + vtkDebugMacro("WARNING: forced to signed int !"); + this->SetDataScalarTypeToInt(); + } + else if ( ImageType == "32S" ) + { + vtkDebugMacro("32 bits signed image"); + this->SetDataScalarTypeToInt(); + } + else if ( ImageType == "FD" ) + { + vtkDebugMacro("64 bits Double image"); + this->SetDataScalarTypeToDouble(); + } + //Set number of scalar components: + this->SetNumberOfScalarComponents(this->NumComponents); + + this->fileTime=this->MTime; + } + + this->Superclass::ExecuteInformation(); } -//---------------------------------------------------------------------------- -// Adds a file name to the internal list of images to read. -void vtkGdcmReader::AddInternalFileName(const char* name) +/* + * Update => ouput->Update => UpdateData => Execute => ExecuteData + * (see vtkSource.cxx for last step). + * This function (redefinition of vtkImageReader::ExecuteData, see + * VTK/IO/vtkImageReader.cxx) reads a data from a file. The datas + * extent/axes are assumed to be the same as the file extent/order. + */ +void vtkGdcmReader::ExecuteData(vtkDataObject *output) { - char * LocalName = new char[strlen(name) + 1]; - strcpy(LocalName, name); - this->InternalFileNameList.push_back(LocalName); - delete[] LocalName; + if (this->InternalFileNameList.empty()) + { + vtkErrorMacro("A least a valid FileName must be specified."); + return; + } + + // FIXME : extraneous parsing of header is made when allocating OuputData + vtkImageData *data = this->AllocateOutputData(output); + data->SetExtent(this->DataExtent); + data->GetPointData()->GetScalars()->SetName("DicomImage-Volume"); + + // Test if output has valid extent + // Prevent memory errors + if((this->DataExtent[1]-this->DataExtent[0]>=0) && + (this->DataExtent[3]-this->DataExtent[2]>=0) && + (this->DataExtent[5]-this->DataExtent[4]>=0)) + { + // The memory size for a full stack of images of course depends + // on the number of planes and the size of each image: + //size_t StackNumPixels = this->NumColumns * this->NumLines + // * this->TotalNumberOfPlanes * this->NumComponents; + //size_t stack_size = StackNumPixels * this->PixelSize; //not used + // Allocate pixel data space itself. + + // Variables for the UpdateProgress. We shall use 50 steps to signify + // the advance of the process: + unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines + * this->TotalNumberOfPlanes + / 50.0); + // The actual advance measure: + unsigned long UpdateProgressCount = 0; + + // Feeling the allocated memory space with each image/volume: + unsigned char *Dest = (unsigned char *)data->GetPointData()->GetScalars()->GetVoidPointer(0); + for (std::list::iterator FileName = InternalFileNameList.begin(); + FileName != InternalFileNameList.end(); + ++FileName) + { + // Images that were tagged as unreadable in CheckFileCoherence() + // are substituted with a black image to let the caller visually + // notice something wrong is going on: + if (*FileName != "GDCM_UNREADABLE") + { + // Update progress related for good files is made in LoadImageInMemory + Dest += this->LoadImageInMemory(*FileName, Dest, + UpdateProgressTarget, + UpdateProgressCount); + } + else + { + // We insert a black image in the stack for the user to be aware that + // this image/volume couldn't be loaded. We simply skip one image + // size: + Dest += this->NumColumns * this->NumLines * this->PixelSize; + + // Update progress related for bad files: + UpdateProgressCount += this->NumLines; + if (UpdateProgressTarget > 0) + { + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } + } + } // Else, file not loadable + } // Loop on files + } } -//---------------------------------------------------------------------------- -// vtkGdcmReader can have the file names specified through two ways: -// (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and -// SetFilePattern() -// (2) By successive calls to vtkGdcmReader::AddFileName() -// When the first method was used by caller we need to update the local -// filename list +/* + * vtkGdcmReader can have the file names specified through two ways: + * (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and + * SetFilePattern() + * (2) By successive calls to vtkGdcmReader::AddFileName() + * When the first method was used by caller we need to update the local + * filename list + */ void vtkGdcmReader::BuildFileListFromPattern() { + this->RemoveAllInternalFileName(); + if ((! this->FileNameList.empty()) && this->FileName ) - { - vtkErrorMacro("Both file patterns and AddFileName schemes were used"); - vtkErrorMacro("Only the files specified with AddFileName shall be used"); - return; - } + { + vtkErrorMacro("Both AddFileName and SetFileName schemes were used"); + vtkErrorMacro("No images loaded ! "); + return; + } + + if ((! this->FileNameList.empty()) && this->FilePrefix ) + { + vtkErrorMacro("Both AddFileName and SetFilePrefix schemes were used"); + vtkErrorMacro("No images loaded ! "); + return; + } + + if (this->FileName && this->FilePrefix) + { + vtkErrorMacro("Both SetFileName and SetFilePrefix schemes were used"); + vtkErrorMacro("No images loaded ! "); + return; + } if (! this->FileNameList.empty() ) - { - vtkDebugMacro("Using the AddFileName specified files"); - this->InternalFileNameList=this->FileNameList; - return; - } - - if (!this->FileName && !this->FilePattern) - { - vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); - vtkErrorMacro("specify a FileName or FilePattern."); - return; - } - - this->RemoveAllInternalFileName(); - for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) - { - this->ComputeInternalFileName(idx); - vtkDebugMacro("Adding file " << this->InternalFileName); - this->AddInternalFileName(this->InternalFileName); - } + { + vtkDebugMacro("Using the AddFileName specified files"); + this->InternalFileNameList=this->FileNameList; + return; + } + + if (!this->FileName && !this->FilePrefix) + { + vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); + vtkErrorMacro("specify a FileName or FilePrefix."); + return; + } + + if( this->FileName ) + { + // Single file loading (as given with ::SetFileName()): + // Case of multi-frame file considered here + this->ComputeInternalFileName(this->DataExtent[4]); + vtkDebugMacro("Adding file " << this->InternalFileName); + this->AddInternalFileName(this->InternalFileName); + } + else + { + // Multi file loading (as given with ::SetFilePattern()): + for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) + { + this->ComputeInternalFileName(idx); + vtkDebugMacro("Adding file " << this->InternalFileName); + this->AddInternalFileName(this->InternalFileName); + } + } } -//---------------------------------------------------------------------------- -// When more than one filename is specified (i.e. we expect loading -// a stack or volume) we need to check that the corresponding images/volumes -// to be loaded are coherent i.e. to make sure: -// - they all share the same X dimensions -// - they all share the same Y dimensions -// - they all share the same ImageType ( 8 bit signed, or unsigned...) -// -// Eventually, we emit a warning when all the files do NOT share the -// Z dimension, since we can still build a stack but the -// files are not coherent in Z, which is probably a source a trouble... -// When files are not readable (either the file cannot be opened or -// because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE". -// This method returns the total number of planar images to be loaded -// (i.e. an image represents one plane, but a volume represents many planes) +/* + * When more than one filename is specified (i.e. we expect loading + * a stack or volume) we need to check that the corresponding images/volumes + * to be loaded are coherent i.e. to make sure: + * - they all share the same X dimensions + * - they all share the same Y dimensions + * - they all share the same ImageType ( 8 bit signed, or unsigned...) + * + * Eventually, we emit a warning when all the files do NOT share the + * Z dimension, since we can still build a stack but the + * files are not coherent in Z, which is probably a source a trouble... + * When files are not readable (either the file cannot be opened or + * because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE". + * This method returns the total number of planar images to be loaded + * (i.e. an image represents one plane, but a volume represents many planes) + */ int vtkGdcmReader::CheckFileCoherence() { - int ReturnedTotalNumberOfPlanes = 0; // The returned value. + int ReturnedTotalNumberOfPlanes = 0; // The returned value. this->BuildFileListFromPattern(); if (this->InternalFileNameList.empty()) - { - vtkErrorMacro("FileNames are not set."); - return 0; - } + { + vtkErrorMacro("FileNames are not set."); + return 0; + } bool FoundReferenceFile = false; int ReferenceNZ = 0; // Loop on the filenames: - // - check for their existence and gdcm "parasability" + // - check for their existence and gdcm "parsability" // - get the coherence check done: - for (std::list::iterator FileName = InternalFileNameList.begin(); - FileName != InternalFileNameList.end(); - ++FileName) - { - // The file is always added in the number of planes - // - If file doesn't exist, it will be replaced by a black place in the - // ExecuteData method - // - If file has more than 1 plane, other planes will be added later to - // to the ReturnedTotalNumberOfPlanes variable counter - ReturnedTotalNumberOfPlanes += 1; - - /////// Stage 0: check for file name: - if(*FileName==std::string("GDCM_UNREADABLE")) - continue; - - /////// Stage 1: check for file readability: - // Stage 1.1: check for file existence. - FILE *fp; - fp = fopen(FileName->c_str(),"rb"); - if (!fp) - { - vtkErrorMacro("Unable to open file " << FileName->c_str()); - vtkErrorMacro("Removing this file from readed files " - << FileName->c_str()); - *FileName = "GDCM_UNREADABLE"; - continue; - } - fclose(fp); - - // Stage 1.2: check for Gdcm parsability - gdcmHeader GdcmHeader(FileName->c_str()); - if (!GdcmHeader.IsReadable()) - { - vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str()); - vtkErrorMacro("Removing this file from readed files " - << FileName->c_str()); - *FileName = "GDCM_UNREADABLE"; - continue; - } - - // Stage 1.3: further gdcm compatibility on PixelType - std::string type = GdcmHeader.GetPixelType(); - if ( (type != "8U") && (type != "8S") - && (type != "16U") && (type != "16S") - && (type != "32U") && (type != "32S") ) - { - vtkErrorMacro("Bad File Type for file" << FileName->c_str()); - vtkErrorMacro("Removing this file from readed files " + for (std::list::iterator FileName = InternalFileNameList.begin(); + FileName != InternalFileNameList.end(); + ++FileName) + { + // The file is always added in the number of planes + // - If file doesn't exist, it will be replaced by a black plane in the + // ExecuteData method + // - If file has more than 1 plane, other planes will be added later to + // to the ReturnedTotalNumberOfPlanes variable counter + ReturnedTotalNumberOfPlanes += 1; + + /////// Stage 0: check for file name: + if(*FileName==std::string("GDCM_UNREADABLE")) + continue; + + /////// Stage 1: check for file readability: + // Stage 1.1: check for file existence. + FILE *fp; + fp = fopen(FileName->c_str(),"rb"); + if (!fp) + { + vtkErrorMacro("Unable to open file " << FileName->c_str()); + vtkErrorMacro("Removing this file from readed files " << FileName->c_str()); - *FileName = "GDCM_UNREADABLE"; - continue; - } - - /////// Stage 2: check coherence of the set of files - int NX = GdcmHeader.GetXSize(); - int NY = GdcmHeader.GetYSize(); - int NZ = GdcmHeader.GetZSize(); - if (FoundReferenceFile) - { - - // Stage 2.1: mandatory coherence stage: - if ( ( NX != this->NumColumns ) - || ( NY != this->NumLines ) - || ( type != this->ImageType ) ) - { - vtkErrorMacro("This file is not coherent with previous ones" - << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; + continue; + } + fclose(fp); + + // Stage 1.2: check for Gdcm parsability + gdcmHeader GdcmHeader(FileName->c_str(), false, true); + // true : for enableSequences + if (!GdcmHeader.IsReadable()) + { + vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str()); vtkErrorMacro("Removing this file from readed files " - << FileName->c_str()); + << FileName->c_str()); *FileName = "GDCM_UNREADABLE"; continue; + } + + // Stage 1.3: further gdcm compatibility on PixelType + std::string type = GdcmHeader.GetPixelType(); + if ( (type != "8U") && (type != "8S") + && (type != "16U") && (type != "16S") + && (type != "32U") && (type != "32S") ) + { + vtkErrorMacro("Bad File Type for file" << FileName->c_str()); + vtkErrorMacro(" " << type.c_str()); + vtkErrorMacro("Removing this file from readed files " + << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; + continue; + } + + // Stage 2: check coherence of the set of files + int NX = GdcmHeader.GetXSize(); + int NY = GdcmHeader.GetYSize(); + int NZ = GdcmHeader.GetZSize(); + if (FoundReferenceFile) + { + // Stage 2.1: mandatory coherence stage: + if ( ( NX != this->NumColumns ) + || ( NY != this->NumLines ) + || ( type != this->ImageType ) ) + { + vtkErrorMacro("This file is not coherent with previous ones" + << FileName->c_str()); + vtkErrorMacro("Removing this file from readed files " + << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; + continue; } - // Stage 2.2: optional coherence stage - if ( NZ != ReferenceNZ ) + // Stage 2.2: optional coherence stage + if ( NZ != ReferenceNZ ) { - vtkErrorMacro("File is not coherent in Z with previous ones" - << FileName->c_str()); + vtkErrorMacro("File is not coherent in Z with previous ones" + << FileName->c_str()); } - else + else { - vtkDebugMacro("File is coherent with previous ones" - << FileName->c_str()); + vtkDebugMacro("File is coherent with previous ones" + << FileName->c_str()); } - // Stage 2.3: when the file contains a volume (as opposed to an image), - // notify the caller. - if (NZ > 1) + // Stage 2.3: when the file contains a volume (as opposed to an image), + // notify the caller. + if (NZ > 1) { - vtkErrorMacro("This file contains multiple planes (images)" - << FileName->c_str()); + vtkErrorMacro("This file contains multiple planes (images)" + << FileName->c_str()); } - // Eventually, this file can be added on the stack. Update the - // full size of the stack - vtkDebugMacro("Number of planes added to the stack: " << NZ); - ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added - continue; - - } else { - // We didn't have a workable reference file yet. Set this one - // as the reference. - FoundReferenceFile = true; - vtkDebugMacro("This file taken as coherence reference:" - << FileName->c_str()); - vtkDebugMacro("Image dimension of reference file as read from Gdcm:" << - NX << " " << NY << " " << NZ); - vtkDebugMacro("Number of planes added to the stack: " << NZ); - // Set aside the size of the image - this->NumColumns = NX; - this->NumLines = NY; - ReferenceNZ = NZ; - ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added - this->ImageType = type; - this->PixelSize = GdcmHeader.GetPixelSize(); - } - } // End of loop on FileName + // Eventually, this file can be added on the stack. Update the + // full size of the stack + vtkDebugMacro("Number of planes added to the stack: " << NZ); + ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added + continue; + + } + else + { + // We didn't have a workable reference file yet. Set this one + // as the reference. + FoundReferenceFile = true; + vtkDebugMacro("This file taken as coherence reference:" + << FileName->c_str()); + vtkDebugMacro("Image dimension of reference file as read from Gdcm:" + << NX << " " << NY << " " << NZ); + vtkDebugMacro("Number of planes added to the stack: " << NZ); + // Set aside the size of the image + this->NumColumns = NX; + this->NumLines = NY; + ReferenceNZ = NZ; + ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added + this->ImageType = type; + this->PixelSize = GdcmHeader.GetPixelSize(); + + if( GdcmHeader.HasLUT() && this->AllowLookupTable ) + { + // I could raise an error is AllowLookupTable is on and HasLUT() off + this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw(); + } + else + { + this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono + } + + //Set image spacing + this->DataSpacing[0] = GdcmHeader.GetXSpacing(); + this->DataSpacing[1] = GdcmHeader.GetYSpacing(); + this->DataSpacing[2] = GdcmHeader.GetZSpacing(); + + //Set image origin + this->DataOrigin[0] = GdcmHeader.GetXOrigin(); + this->DataOrigin[1] = GdcmHeader.GetYOrigin(); + this->DataOrigin[2] = GdcmHeader.GetZOrigin(); + + } + } // End of loop on FileName ///////// The files we CANNOT load are flaged. On debugging purposes - // count the loadable number of files and display thir number: + // count the loadable number of files and display their number: int NumberCoherentFiles = 0; - for (std::list::iterator Filename = InternalFileNameList.begin(); - Filename != InternalFileNameList.end(); - ++Filename) - { + for (std::list::iterator Filename = InternalFileNameList.begin(); + Filename != InternalFileNameList.end(); + ++Filename) + { if (*Filename != "GDCM_UNREADABLE") NumberCoherentFiles++; - } + } vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles); if (ReturnedTotalNumberOfPlanes == 0) - { - vtkErrorMacro("No loadable file."); - } + { + vtkErrorMacro("No loadable file."); + } vtkDebugMacro("Total number of planes on the stack: " - << ReturnedTotalNumberOfPlanes); + << ReturnedTotalNumberOfPlanes); - return ReturnedTotalNumberOfPlanes; + return ReturnedTotalNumberOfPlanes; } -//---------------------------------------------------------------------------- -// Configure the output e.g. WholeExtent, spacing, origin, scalar type... -void vtkGdcmReader::ExecuteInformation() +//----------------------------------------------------------------------------- +// Private +/* + * Remove all file names to the internal list of images to read. + */ +void vtkGdcmReader::RemoveAllInternalFileName(void) { - this->TotalNumberOfPlanes = this->CheckFileCoherence(); - if ( this->TotalNumberOfPlanes == 0) - { - vtkErrorMacro("File set is not coherent. Exiting..."); - return; - } - - // if the user has not set the extent, but has set the VOI - // set the zaxis extent to the VOI z axis - if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 && - (this->DataVOI[4] || this->DataVOI[5])) - { - this->DataExtent[4] = this->DataVOI[4]; - this->DataExtent[5] = this->DataVOI[5]; - } - - // When the user has set the VOI, check it's coherence with the file content. - if (this->DataVOI[0] || this->DataVOI[1] || - this->DataVOI[2] || this->DataVOI[3] || - this->DataVOI[4] || this->DataVOI[5]) - { - if ((this->DataVOI[0] < 0) || - (this->DataVOI[1] >= this->NumColumns) || - (this->DataVOI[2] < 0) || - (this->DataVOI[3] >= this->NumLines) || - (this->DataVOI[4] < 0) || - (this->DataVOI[5] >= this->TotalNumberOfPlanes )) - { - vtkWarningMacro("The requested VOI is larger than expected extent."); - this->DataVOI[0] = 0; - this->DataVOI[1] = this->NumColumns - 1; - this->DataVOI[2] = 0; - this->DataVOI[3] = this->NumLines - 1; - this->DataVOI[4] = 0; - this->DataVOI[5] = this->TotalNumberOfPlanes - 1; - } - } - - // Positionate the Extent. - this->DataExtent[0] = 0; - this->DataExtent[1] = this->NumColumns - 1; - this->DataExtent[2] = 0; - this->DataExtent[3] = this->NumLines - 1; - if(this->InternalFileNameList.size() > 1) - { - this->DataExtent[4] = 0; - this->DataExtent[5] = this->TotalNumberOfPlanes - 1; - } - - // We don't need to positionate the Endian related stuff (by using - // this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian() - // since the reading of the file is done by gdcm. - // But we do need to set up the data type for downstream filters: - if ( ImageType == "8U" ) - { - vtkDebugMacro("8 bits unsigned image"); - this->SetDataScalarTypeToUnsignedChar(); - } - else if ( ImageType == "8S" ) - { - vtkErrorMacro("Cannot handle 8 bit signed files"); - return; - } - else if ( ImageType == "16U" ) - { - vtkDebugMacro("16 bits unsigned image"); - this->SetDataScalarTypeToUnsignedShort(); - } - else if ( ImageType == "16S" ) - { - vtkDebugMacro("16 bits signed image"); - this->SetDataScalarTypeToShort(); - //vtkErrorMacro("Cannot handle 16 bit signed files"); - } - else if ( ImageType == "32U" ) - { - vtkDebugMacro("32 bits unsigned image"); - vtkDebugMacro("WARNING: forced to signed int !"); - this->SetDataScalarTypeToInt(); - } - else if ( ImageType == "32S" ) - { - vtkDebugMacro("32 bits signed image"); - this->SetDataScalarTypeToInt(); - } - - vtkImageReader::ExecuteInformation(); + this->InternalFileNameList.clear(); +} + +/* + * Adds a file name to the internal list of images to read. + */ +void vtkGdcmReader::AddInternalFileName(const char* name) +{ + char * LocalName = new char[strlen(name) + 1]; + strcpy(LocalName, name); + this->InternalFileNameList.push_back(LocalName); + delete[] LocalName; } -//---------------------------------------------------------------------------- -// Loads the contents of the image/volume contained by Filename at -// the Dest memory address. Returns the size of the data loaded. +/* + * Loads the contents of the image/volume contained by Filename at + * the Dest memory address. Returns the size of the data loaded. + */ size_t vtkGdcmReader::LoadImageInMemory( std::string FileName, unsigned char * Dest, const unsigned long UpdateProgressTarget, unsigned long & UpdateProgressCount) { - vtkDebugMacro("Copying to memmory image" << FileName.c_str()); - gdcmFile GdcmFile(FileName.c_str()); - size_t size = GdcmFile.GetImageDataSize(); - - // If the data structure of vtk for image/volume representation - // were straigthforwards the following would suffice: - // GdcmFile.GetImageDataIntoVector((void*)Dest, size); - // But vtk chose to invert the lines of an image, that is the last - // line comes first (for some axis related reasons?). Hence we need - // to load the image line by line, starting from the end: - int NumColumns = GdcmFile.GetXSize(); - int NumLines = GdcmFile.GetYSize(); - int NumPlanes = GdcmFile.GetZSize(); - int LineSize = NumColumns * GdcmFile.GetPixelSize(); - unsigned char * Source = (unsigned char*)GdcmFile.GetImageData(); - unsigned char * pSource = Source; //pointer for later deletion - unsigned char * Destination = Dest + size - LineSize; - - for (int plane = 0; plane < NumPlanes; plane++) - { - for (int line = 0; line < NumLines; line++) - { - // Copy one line at proper destination: - memcpy((void*)Destination, (void*)Source, LineSize); - Source += LineSize; - Destination -= LineSize; - // Update progress related: - if (!(UpdateProgressCount%UpdateProgressTarget)) - { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); - } - UpdateProgressCount++; - } - } - //GetImageData allocate a (void*)malloc, remove it: - free(pSource); + vtkDebugMacro("Copying to memory image [" << FileName.c_str() << "]"); + gdcmFile GdcmFile(FileName.c_str(),false,true); + // true : to enable SeQuences + size_t size; + + // If the data structure of vtk for image/volume representation + // were straigthforwards the following would be enough: + // GdcmFile.GetImageDataIntoVector((void*)Dest, size); + // But vtk chooses to invert the lines of an image, that is the last + // line comes first (for some axis related reasons?). Hence we need + // to load the image line by line, starting from the end. + + int NumColumns = GdcmFile.GetHeader()->GetXSize(); + int NumLines = GdcmFile.GetHeader()->GetYSize(); + int NumPlanes = GdcmFile.GetHeader()->GetZSize(); + int LineSize = NumComponents * NumColumns * GdcmFile.GetHeader()->GetPixelSize(); + + unsigned char * Source; + + if( GdcmFile.GetHeader()->HasLUT() && this->AllowLookupTable ) + { + size = GdcmFile.GetImageDataSizeRaw(); + Source = (unsigned char*) GdcmFile.GetImageDataRaw(); + unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA(); - return size; -} + if(!this->LookupTable) + this->LookupTable = vtkLookupTable::New(); -//---------------------------------------------------------------------------- -// Update => ouput->Update => UpdateData => Execute => ExecuteData -// (see vtkSource.cxx for last step). -// This function (redefinition of vtkImageReader::ExecuteData, see -// VTK/IO/vtkImageReader.cxx) reads a data from a file. The datas -// extent/axes are assumed to be the same as the file extent/order. -void vtkGdcmReader::ExecuteData(vtkDataObject *output) -{ - if (this->InternalFileNameList.empty()) - { - vtkErrorMacro("A least a valid FileName must be specified."); - return; - } - - // FIXME : extraneous parsing of header is made when allocating OuputData - vtkImageData *data = this->AllocateOutputData(output); - data->SetExtent(this->DataExtent); - data->GetPointData()->GetScalars()->SetName("DicomImage-Volume"); - - // Test if output has valid extent - // Prevent memory errors - if((this->DataExtent[1]-this->DataExtent[0]>=0) && - (this->DataExtent[3]-this->DataExtent[2]>=0) && - (this->DataExtent[5]-this->DataExtent[4]>=0)) - { - // The memory size for a full stack of images of course depends - // on the number of planes and the size of each image: - size_t StackNumPixels = this->NumColumns * this->NumLines - * this->TotalNumberOfPlanes; - size_t stack_size = StackNumPixels * this->PixelSize; - // Allocate pixel data space itself. - unsigned char *mem = new unsigned char [stack_size]; - - // Variables for the UpdateProgress. We shall use 50 steps to signify - // the advance of the process: - unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines - * this->TotalNumberOfPlanes - / 50.0); - // The actual advance measure: - unsigned long UpdateProgressCount = 0; - - // Feeling the allocated memory space with each image/volume: - unsigned char * Dest = mem; - for (std::list::iterator FileName = InternalFileNameList.begin(); - FileName != InternalFileNameList.end(); - ++FileName) - { - // Images that were tagged as unreadable in CheckFileCoherence() - // are substituted with a black image to let the caller visually - // notice something wrong is going on: - if (*FileName != "GDCM_UNREADABLE") - { - // Update progress related for good files is made in LoadImageInMemory - Dest += this->LoadImageInMemory(*FileName, Dest, - UpdateProgressTarget, - UpdateProgressCount); - } else { - // We insert a black image in the stack for the user to be aware that - // this image/volume couldn't be loaded. We simply skip one image - // size: - Dest += this->NumColumns * this->NumLines * this->PixelSize; - - // Update progress related for bad files: - UpdateProgressCount += this->NumLines; - if (UpdateProgressTarget > 0) - { - if (!(UpdateProgressCount%UpdateProgressTarget)) - { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); - } - } - } // Else, file not loadable - } // Loop on files + this->LookupTable->SetNumberOfTableValues(256); + for (int tmp=0; tmp<256; tmp++) + { + this->LookupTable->SetTableValue(tmp, + (float)Lut[4*tmp+0]/255.0, + (float)Lut[4*tmp+1]/255.0, + (float)Lut[4*tmp+2]/255.0, + 1); + } + this->LookupTable->SetRange(0,255); + vtkDataSetAttributes *a=this->GetOutput()->GetPointData(); + a->GetScalars()->SetLookupTable(this->LookupTable); + free(Lut); + } + else + { + size = GdcmFile.GetImageDataSize(); + Source = (unsigned char*)GdcmFile.GetImageData(); + } + + unsigned char * pSource = Source; //pointer for later deletion + unsigned char * Destination = Dest + size - LineSize; - // The "size" of the vtkScalars data is expressed in number of points, - // and is not the memory size representing those points: - data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0); - this->Modified(); - } + for (int plane = 0; plane < NumPlanes; plane++) + { + for (int line = 0; line < NumLines; line++) + { + // Copy one line at proper destination: + memcpy((void*)Destination, (void*)Source, LineSize); + Source += LineSize; + Destination -= LineSize; + // Update progress related: + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } + UpdateProgressCount++; + } + } + +// DO NOT remove this commented out code . +// Nobody knows what's expecting you ... +// Just to 'see' what was actually read on disk :-( + +// FILE * f2; +// f2 = fopen("SpuriousFile.RAW","wb"); +// fwrite(Dest,size,1,f2); +// fclose(f2); + + //GetImageData allocate a (void*)malloc, remove it: + delete[] pSource; + return size; } -//---------------------------------------------------------------------------- -void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) -{ - vtkImageReader::PrintSelf(os,indent); - os << indent << "Filenames : " << endl; - vtkIndent nextIndent = indent.GetNextIndent(); - for (std::list::iterator FileName = FileNameList.begin(); - FileName != FileNameList.end(); - ++FileName) - { - os << nextIndent << FileName->c_str() << endl ; - } -} +//-----------------------------------------------------------------------------